Some non-cohort columns are added to the cohort table
tables = list(
"cohort" = dplyr::tibble(
cohort_definition_id = 1L,
subject_id = c(1, 2, 3, 4, 4) |> as.integer(),
cohort_start_date = as.Date(c("2000-06-03", "2000-01-01", "2015-01-15", "1989-12-09", "2000-12-09")),
cohort_end_date = as.Date(c("2001-09-01", "2001-01-12", "2015-02-15", "1990-12-09", "2002-12-09")),
other_date_1 = as.Date(c("2001-08-01", "2001-01-01", "2015-01-15", NA, "2002-12-09")),
other_date_2 = as.Date(c("2001-08-01", NA, "2015-04-15", "1990-11-09", "2002-12-09"))
)
)
cdm <- omock::mockCdmFromTables(tables = tables, seed = 1)
#> Warning: ! 9 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `cdm_version` is numeric but expected character
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: ! 1 column in vocabulary do not match expected column type:
#> • `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 5 column in concept_relationship do not match expected column type:
#> • `concept_id_1` is numeric but expected integer
#> • `concept_id_2` is numeric but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 2 column in concept_synonym do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `language_concept_id` is numeric but expected integer
#> Warning: ! 4 column in concept_ancestor do not match expected column type:
#> • `ancestor_concept_id` is numeric but expected integer
#> • `descendant_concept_id` is numeric but expected integer
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 9 column in drug_strength do not match expected column type:
#> • `drug_concept_id` is numeric but expected integer
#> • `ingredient_concept_id` is numeric but expected integer
#> • `amount_unit_concept_id` is numeric but expected integer
#> • `numerator_unit_concept_id` is numeric but expected integer
#> • `denominator_value` is logical but expected numeric
#> • `denominator_unit_concept_id` is numeric but expected integer
#> • `box_size` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
cdm$cohort
#> # A tibble: 5 × 12
#> cohort_definition_id subject_id cohort_start_date cohort_end_date other_date_1
#> <int> <int> <date> <date> <date>
#> 1 1 1 2000-06-03 2001-09-01 2001-08-01
#> 2 1 2 2000-01-01 2001-01-12 2001-01-01
#> 3 1 3 2015-01-15 2015-02-15 2015-01-15
#> 4 1 4 1989-12-09 1990-12-09 NA
#> 5 1 4 2000-12-09 2002-12-09 2002-12-09
#> # ℹ 7 more variables: other_date_2 <date>, cohort_definition_name <chr>,
#> # cohort_definition_description <chr>, definition_type_concept_id <int>,
#> # cohort_definition_syntax <chr>, subject_concept_id <int>,
#> # cohort_initiation_date <date>
Some non-cohort columns are added to the cohort table
Created on 2024-10-16 with reprex v2.1.1